In 1965, the Graduate School of Business Administration was established to strengthen corporate competitiveness and contribute to the national economic development through the education of leaders in the government and private sector who wanted to pursue additional studies in business and economics. The need to establish a specialized educational institution to nourish professional economists with required expertise eventually led to the establishment of the Graduate School of Economics, a separate graduate school in 1998.

Currently, the Graduate School of Economics has a master's degree program with the following five majors: (1) financial engineering, (2) insurance, (3) trade and industry, (4) public economics and economic development and (5) corporate economics. The school also maintains the nation’s only Advanced Economists Program (AEP). The school has produced approximately 1,800 alumni from the master's program and 1,300 from AEP who are now contributing greatly to the economic development by actively exploring their area of specialization. In addition, the school regularly holds the Global Economic Forum and special lectures from invited speakers every semester. At the end of the year, the school awards the "Honorable Yonsei Economists" award to a select number of alumni among the graduates from the master's program and AEP.